hyperClust

This software is described in detail in our published analysis.

Overview

hyperClust is a pipeline for detection of somatic local hyper-mutation (mutation clusters). In brief, mutations that are located closer than expected to their nearest neighbor (closest adjacent mutation) are considered clusters of mutagenesis. These clusters can have different characteristics and be generated from a sort of different mutational processes.

The pipeline is built in nextflow, a pipeline framework for reproducible research. The software handles parallelization in multiple HPC scheduler or multicore machine. See installation for more details.

Installation

Requirements

A Unix system plus a nextflow installation is required, other required software is listed here.

Installation instructions for these tools are available in each site.

Usage

Install requirements
Build index files
Mask the reference genome
Run the pipeline

nextflow run davidmasp/hyperclust \
    -profile slurm,conda \
    -w /path/to/scratch \
    -resume \
    -N you@gmail.com \
    --index index.csv \
    --genome refseq.fa

Documentation

A brief documentation can be found in the docs/ directory.

Please, if you find any issue or question report it in the issue section.

Credit

Author: David Mas-Ponte